muscle

TAFFISH wrapper for MUSCLE 5, software for multiple sequence alignment, alignment ensembles, and Reseek-based structure alignment inputs.

This app packages upstream MUSCLE v5.3 as 5.3-r4. The container builds from the upstream source tag rather than copying the release binaries, because the official muscle-aarch64.v5.3 Linux asset fails immediately on linux/arm64 with a pointer-size assertion. The TAFFISH build applies one small portability patch: Linux __aarch64__ is recognized as a 64-bit platform. It also removes -march=native from the generated Makefile so the static binary is not tied to the build host CPU.

Release 5.3-r4 is a follow-up license-metadata TAFFISH update. It keeps the upstream source, runtime dependencies, smoke coverage, help text, and command behavior unchanged while keeping the app/upstream license boundary fixed. Because this is metadata-only, the upstream runtime version string remains muscle 5.3.linux64 [v5.3-taffish-r2].

Package metadata:

name: muscle
command: taf-muscle
version: 5.3-r4
kind: tool
image: ghcr.io/taffish/muscle:5.3-r4
upstream release: v5.3
upstream runtime version: muscle 5.3.linux64 [v5.3-taffish-r2]

Install

taf install muscle

Then run:

taf-muscle --help
taf-muscle --version
taf-muscle -- -version
taf-muscle muscle -version

taf-muscle --help shows TAFFISH wrapper help. Use -- when the first upstream argument starts with -, for example taf-muscle -- -h or taf-muscle -- -version. Command mode is also available: taf-muscle muscle -version.

Examples

Align FASTA input:

taf-muscle -- -align input.fa -output aln.afa

Use Super5 for large inputs:

taf-muscle -- -super5 input.fa -output aln.afa

Generate a small diversified ensemble in EFA format:

taf-muscle -- -align input.fa -diversified -replicates 100 -output ensemble.efa

Extract a representative alignment and split an EFA file:

taf-muscle -- -maxcc ensemble.efa -output maxcc.afa
taf-muscle -- -efa_explode ensemble.efa

Structure alignment is supported by upstream MUSCLE 5.3 when users provide Reseek-generated mega and, for -super7, distance-matrix inputs:

taf-muscle -- -align structs.mega -output structs.afa
taf-muscle -- -super7 structs.mega -distmxin structs.distmx -reseek -output structs.afa

This app does not bundle reseek; generate those files with a separate Reseek installation or app.

Platform

The image is built for native linux/amd64 and linux/arm64. The MUSCLE binary is statically linked, so it has no dynamic library dependency beyond the Linux kernel ABI.

Package contents are intentionally small: the runtime image ships the muscle executable plus upstream README, LICENSE, a version marker, and a TAFFISH_PATCHES note. A source scan found no runtime system, popen, or exec-style helper calls in the MUSCLE C++ code; the vcxproj_make.py helper is used only while building the image and is not part of the runtime path.

Runtime version output is:

muscle 5.3.linux64 [v5.3-taffish-r2]

The linux64 platform label is MUSCLE's upstream label for 64-bit Linux builds; it is used for both amd64 and arm64 here.

Smoke Coverage

Smoke tests check:

• package version marker and upstream muscle -version;
• help text for FASTA alignment and EFA ensemble features;
• static-link status with ldd;
• a tiny -align FASTA-to-AFA path;
• a tiny -super5 path;
• a tiny ensemble path using -diversified, -maxcc, -resample, and -efa_explode.

These checks verify packaging and representative core paths. They do not replace large biological benchmarks, memory-scaling tests, or validation of Reseek-generated structure-alignment inputs.

Boundaries

This app packages MUSCLE only. It does not include Reseek, PDB/mmCIF fetching, tree-building tools, downstream phylogenetic software, or large benchmark datasets. MUSCLE can consume structure-alignment inputs generated elsewhere, but this app does not create those inputs by itself.

License Boundary

The TAFFISH app packaging files are licensed under Apache-2.0. The packaged upstream MUSCLE software is covered by: GPL-3.0. Bundled third-party components, datasets, models, and external resources keep their own license terms.

Upstream

• Upstream repository: https://github.com/rcedgar/muscle
• MUSCLE 5 home page: https://drive5.com/muscle5/
• Release: https://github.com/rcedgar/muscle/releases/tag/v5.3
• Upstream license: GPL-3.0
• Citation: Edgar RC. 2022. Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny. Nature Communications 13, 6968.
• DOI: https://doi.org/10.1038/s41467-022-34630-w
• PMID: 36379955

MUSCLE 5.3 also includes Muscle-3D support described by Edgar and Tolstoy 2024, bioRxiv DOI https://doi.org/10.1101/2024.10.26.620413.